+Open data
-Basic information
Entry | Database: PDB / ID: 6i1z | ||||||
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Title | Outward facing structure of apo CST | ||||||
Components | CMP-sialic acid transporter 1 | ||||||
Keywords | MEMBRANE PROTEIN / CMP-sialic acid transporter / Secondary active transporter / Nucleotide sugar transporter / SLC35A1 | ||||||
Function / homology | pyrimidine nucleotide-sugar transmembrane transporter activity / Nucleotide-sugar transporter / Nucleotide-sugar transporter / sialic acid transmembrane transporter activity / Golgi membrane / identical protein binding / CMP-sialic acid transporter 1 Function and homology information | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Nji, E. / Gulati, A. / Qureshi, A.A. / Drew, D. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2019 Title: Structural basis for the delivery of activated sialic acid into Golgi for sialyation. Authors: Nji, E. / Gulati, A. / Qureshi, A.A. / Coincon, M. / Drew, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i1z.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i1z.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 6i1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i1z_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
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Full document | 6i1z_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 6i1z_validation.xml.gz | 22 KB | Display | |
Data in CIF | 6i1z_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/6i1z ftp://data.pdbj.org/pub/pdb/validation_reports/i1/6i1z | HTTPS FTP |
-Related structure data
Related structure data | 6i1rSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 312 / Label seq-ID: 2 - 312
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-Components
#1: Protein | Mass: 36518.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: 100274139, ZEAMMB73_Zm00001d046060 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B4FZ94 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 73.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 35 % (v/v) PEG 400, 0.1 M NaCl, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→47.77 Å / Num. obs: 17696 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.984 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.052 / Rrim(I) all: 0.133 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 3.4→3.68 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.323 / Num. unique obs: 3623 / CC1/2: 0.532 / Rpim(I) all: 0.59 / Rrim(I) all: 1.458 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I1R Resolution: 3.4→21.95 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.927 / SU B: 38.353 / SU ML: 0.549 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 390.14 Å2 / Biso mean: 161.973 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 3.4→21.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8636 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3.404→3.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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